how the pipeline for analysing whole genome of bacteria looks like?

Hello,

Actually I would like to have a big picture of what a pipeline for whole genome of bacteria is!

This helps me to better understand the steps one can follow and what needs to be improved

If you are also aware of any good paper related, you can post it here too please.

Thanks

rna-seq bacteria

• 1,968 views • link

updated 4.1 years ago by Ram

• written 11.4 years ago by Mo

1 answer

Please have a look

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042304

http://genomebiology.com/2013/14/1/r2

http://www.biomedcentral.com/1471-2105/15/126

Hope you will get an idea.

• 0 views • link

written 11.4 years ago by HG

More posts like this

Reference request for getting the big picture of gene taxonomy
written 3.2 years ago by garbagelister •

Hello, my background is in computer science. I have studied a bit of biology on my own, but nothing deep. I would like to find …
Inquiry related to inverse quantile normalization
written 4.0 years ago by rheab1230 •

Hello everyone, I want to ask in order to do inverse quantile normalization using the gtex pipeline: https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl eqtl_prepare_expression.py ${tpm_gct} ${counts_gct} ${annotation_gtf} \ ${sample_participant_lookup} ${vcf_chr_list} …
Issue with ncbi ftp server
written 4.7 years ago by Sharon •

Hello, I have been trying to access the RefSeq of a bacteria using this link: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/ however I am unable to gain access. The email …
blastn for global alignment
written 5.1 years ago by obalasz.spam •

Hello guys, do you know an approach or settings in blastn, that helps to align more-or-less the full query sequence against a target sequence? I …
Removal of unwanted character "N" from Assambly and Annotated file of whole genome sequemce
written 6.8 years ago by tasmina.fm •

We are working with assembly and annotation of whole genome sequence of bacteria with Linux command (soapdenovo2 and some related software). After assembly and annotation, …
Forum: SSD or HHD for genome analysis
written 6.8 years ago by Neil •

Hello. I need to analysis mostly human whole exomes and far less frequently human whole genomes. And today, I must choose what is better for …
What does LnP(D) per clusters K plot means?
written 7.5 years ago by rimgubaev

Hello everyone! I am new to GWAS analysis and currently read some papers related to it. I saw such a plot (LnP(D) per clusters K) …
Coverage depth and breadth after recaliberation
written 10.6 years ago by nikkihathi •

Hello! My question is related to the coverage of reads at two steps first, after mapping and second post-alignment processing. The main aim of my …
RNA-seq: how big should be the library?
written 11.3 years ago by Aurelie MLB

Hello, I am wondering how big should be the library for each sample to big enough to detect meaningful differential expression please? Is 15M reads …
Rate Of Evolution, Gc Content, Codon Usage And Rate Of Amino Acid Substitution
written 12.7 years ago by Pappu

<p>While trying to understand the evolution of a gene, I encountered the aforementioned variables. I am wondering how the interplay of these variables contribute to …